[med-svn] [htslib] 04/10: regidx: simple file format autodetection

[Charles Plessy]

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plessy pushed a commit to branch debian/unstable
in repository htslib.

commit d2cb7bacc15bd20960e89cf46712551657512adb
Author: Petr Danecek <pd3 at sanger.ac.uk>
Date:   Wed Oct 1 13:15:42 2014 +0100

    regidx: simple file format autodetection
---
 htslib/regidx.h |  5 ++++-
 regidx.c        | 15 +++++++++++++++
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/htslib/regidx.h b/htslib/regidx.h
index 74dc8c7..69f0812 100644
--- a/htslib/regidx.h
+++ b/htslib/regidx.h
@@ -93,7 +93,10 @@ int regidx_parse_tab(const char*,char**,char**,reg_t*,void*,void*);   // CHROM,P
 /*
  *  regidx_init() - creates new index
  *  @param fname:  input file name or NULL if regions will be added one-by-one via regidx_insert()
- *  @param parsef: regidx_parse_bed, regidx_parse_tab or see description of regidx_parse_f
+ *  @param parsef: regidx_parse_bed, regidx_parse_tab or see description of regidx_parse_f. If NULL,
+ *                 the format will be autodected, currently either regidx_parse_tab (the default) or
+ *                 regidx_parse_bed (file must be named 'bed' or 'bed.gz') will be used. Note that
+ *                 the exact autodetection algorithm will change.
  *  @param freef:  NULL or see description of regidx_parse_f
  *  @param payload_size: 0 with regidx_parse_bed, regidx_parse_tab or see regidx_parse_f
  *  @param usr:    optional user data passed to regidx_parse_f
diff --git a/regidx.c b/regidx.c
index 5dd3b0e..ac6562c 100644
--- a/regidx.c
+++ b/regidx.c
@@ -150,6 +150,21 @@ int regidx_insert(regidx_t *idx, char *line)
 
 regidx_t *regidx_init(const char *fname, regidx_parse_f parser, regidx_free_f free_f, ssize_t payload_size, void *usr_dat)
 {
+    if ( !parser )
+    {
+        if ( !fname ) parser = regidx_parse_tab;
+        else
+        {
+            int len = strlen(fname);
+            if ( len>=7 && !strcasecmp(".bed.gz",fname+len-7) )
+                parser = regidx_parse_bed;
+            else if ( len>=4 && !strcasecmp(".bed",fname+len-4) )
+                parser = regidx_parse_bed;
+            else
+                parser = regidx_parse_tab;
+        }
+    }
+
     regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t));
     idx->free  = free_f;
     idx->parse = parser;

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